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How can I keep track of changes to the code?

The FieldTrip code is accessible using git at github.com. To quickly get access to the code, you would do the following from the command line or the equivalent in a graphical git interface, such as the GitHub desktop.

git clone https://github.com/fieldtrip/fieldtrip

To update automatically, you could schedule a job (e.g. using cron) to run “git pull” every night.